Originally Posted by Shake'n'Bake

We may have a problem with clarity, I assume by thighs that you mean quads (the muscles on the front of the upper leg) not the hamstring, the muscle on the back of the upper leg. DScott is correct that moving the saddle back should put more emphasis on the hamstring, especially when climbing. If you want to put more emphasis on the hamstring then the fore and aft position of the cleat is less important than the position of the saddle.

Properly adjusting one's cleats is a very complicated proposition, but in general moving the cleat back will put more emphasis on the quads. It will also promote a more heels down pedalstroke, and a lower cadence. In general this is not the recommended setup. Time trialers can get away with this setup, but the current theory is to have the cleat a little more forward to promote higher rpm's. If you do move the cleat back then you should lower the saddle a fraction, and slide it forward a touch. There is actually a ratio to how much you should lower the saddle for each mm movement of the cleat, but I don't recall what it is. But most people don't have their setup so finely tuned that these minor adjustments will be noticeable.

The important question is, should you adjust your cleats to emphasize your thighs? I have no way of knowing without evaluating your entire physiology. Usually it's as simple as looking at someone to determine what setup will work best for them. Tall skinny climbers like Rasmussen need a different setup than short powerful riders like Hinault or Ulrich. Lance and Indurain had the perfect physique, halfway between a climber and a masher. But if you really think that emphasizing your thighs is the best way to go for your particular physiology, then it should be as simple as moving the cleats back 3mm or so.

You can check your current positioning by sitting on your bike with the pedals parallel to the ground. Then drop a plumb line down from your forward knee, (Actualy the boney protrusion below your kneecap) The line should fall right at the pedal spindle. That would be a fairly neutral position. You can adjust the saddle forward or back from there, depending upon what muscle groups you wish to emphasize. Forward for the quads and lower rpm's, back for the hamstrings and higher rpm's.

These are just general guidelines and everyone's physiology is different. Some of us never seem to get the setup quite right.

But hopefully this helped you more than it confused you.